Mon Oct 10 13:59:17 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:59:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6051129 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -10.36400 34.99700 ymin,ymax (A): 0.4460000 41.05800 zmin,zma (A): -30.64600 28.18600 x,y,z range (A): 45.36100 40.61200 58.83200 scale (grids/A): 0.6051129 object centre (A): 12.31650 20.75200 -1.230000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000008 assigned positive charge : 287.5790 centred at (gu) : 89.54105 89.52682 90.56912 assigned negative charge : -283.5793 centred at (gu) : 89.61799 89.63929 90.59158 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4807 nv = 96 ne = 84 npr = 40718 no. pairs analyzed = 40718 no. exposed pairs = 2491 no. arc points = 17374 no. surface atoms = 845 nbur = 1115 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 222 mr = 2605 m= 0 mr = 19 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1759 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5886 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3788977E-09 1.4608654E-09 midg,1,midg; midg,igrid,midg 6.0770975E-09 -1.3870769E-09 1,midg,midg; igrid,midg,midg 4.8522764E-09 -3.7227557E-10 gauss-seidel spectral radius is 0.9858075 estimated iterations to convergence 69 setup time was (sec) 0.3600000 now iterating at: 13:59:18 rms-change max change #iterations 9.6356899E-02 17.17402 at 10iterations 8.1348345E-03 1.527925 at 20iterations 6.9693360E-04 0.1090269 at 30iterations 6.0495811E-05 1.1791229E-02 at 40iterations 5.1718498E-06 8.8882446E-04 at 50iterations finished qdiffx linear iterations at : 13:59:21 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.1718498E-06 8.8882446E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 13:59:22 3.418u 0.181s 0:04.74 75.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:59:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.815339 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -10.36400 34.99700 ymin,ymax (A): 0.4460000 41.05800 zmin,zma (A): -30.64600 28.18600 x,y,z range (A): 45.36100 40.61200 58.83200 scale (grids/A): 1.815339 object centre (A): 12.31650 20.75200 -1.230000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000008 assigned positive charge : 287.5790 centred at (gu) : 88.62276 88.58047 91.70748 assigned negative charge : -283.5793 centred at (gu) : 88.85410 88.91813 91.77495 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 51677 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17374 grid for indexing accessible points = 1.400000 m= 17457 mr = 35155 m= 2303 mr = 12844 m= 110 mr = 1367 m= 0 mr = 38 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 390 time to turn everything in is 0.2600000 number of dielectric boundary points 22143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14290 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6051129 object centre at (A) : 12.31650 20.75200 -1.230000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5461581E-02 2.2550641E-02 midg,1,midg; midg,igrid,midg 5.0812261E-03 -1.0488153E-03 1,midg,midg; igrid,midg,midg -1.7729810E-03 -2.2059842E-03 gauss-seidel spectral radius is 0.9984207 estimated iterations to convergence 200 setup time was (sec) 0.4900000 now iterating at: 13:59:23 rms-change max change #iterations 3.195338 182.1688 at 10iterations 1.414401 59.24586 at 20iterations 0.6266162 27.64033 at 30iterations 0.2750358 10.74130 at 40iterations 0.1218462 4.870528 at 50iterations 5.3870108E-02 1.926774 at 60iterations 2.3798170E-02 0.8914657 at 70iterations 1.0494794E-02 0.4018430 at 80iterations 4.6561370E-03 0.1906679 at 90iterations 2.0446754E-03 8.4963799E-02 at 100iterations 9.0910145E-04 3.4212112E-02 at 110iterations 4.0109520E-04 1.4028549E-02 at 120iterations finished qdiffx linear iterations at : 13:59:30 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 4.0109520E-04 1.4028549E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 13:59:31 7.897u 0.237s 0:08.91 91.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:59:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.723008 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -10.36400 34.99700 ymin,ymax (A): 0.4460000 41.05800 zmin,zma (A): -30.64600 28.18600 x,y,z range (A): 45.36100 40.61200 58.83200 scale (grids/A): 2.723008 object centre (A): 12.31650 20.75200 -1.230000 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000008 assigned positive charge : 287.5790 centred at (gu) : 87.93414 87.87075 92.56112 assigned negative charge : -283.5793 centred at (gu) : 88.28120 88.37724 92.66240 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 119530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17374 grid for indexing accessible points = 1.400000 m= 58140 mr = 85261 m= 19372 mr = 47467 m= 3979 mr = 15625 m= 435 mr = 2858 m= 18 mr = 265 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1268 time to turn everything in is 0.6800000 number of dielectric boundary points 49990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14622 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.815339 object centre at (A) : 12.31650 20.75200 -1.230000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1775134 0.1333928 midg,1,midg; midg,igrid,midg 1.8880552E-02 -1.9848086E-02 1,midg,midg; igrid,midg,midg -5.9929010E-02 -4.8280161E-02 gauss-seidel spectral radius is 0.9991814 estimated iterations to convergence 276 setup time was (sec) 0.9500000 now iterating at: 13:59:33 rms-change max change #iterations 7.693773 259.3904 at 10iterations 4.337036 113.5502 at 20iterations 2.429469 56.10585 at 30iterations 1.356324 34.74026 at 40iterations 0.7561668 15.99481 at 50iterations 0.4204037 9.652967 at 60iterations 0.2337756 5.097148 at 70iterations 0.1299729 2.853143 at 80iterations 7.2528854E-02 1.533689 at 90iterations 4.0301584E-02 0.8697510 at 100iterations 2.2439919E-02 0.4764366 at 110iterations 1.2524089E-02 0.2834892 at 120iterations 6.9687334E-03 0.1454544 at 130iterations 3.8612762E-03 8.4731102E-02 at 140iterations 2.1597515E-03 4.5204163E-02 at 150iterations 1.2018697E-03 2.6788712E-02 at 160iterations 6.6782604E-04 1.4114380E-02 at 170iterations 3.7211430E-04 8.0425739E-03 at 180iterations finished qdiffx linear iterations at : 13:59:45 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 3.7211430E-04 8.0425739E-03 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 13:59:46 13.209u 0.288s 0:14.47 93.1% 0+0k 0+0io 0pf+0w